Plot holes (spoilers included) in RotE

[Brashen]

Another possible plot hole or contradiction is malta's escape from fregong.
The river has risen considerably since the last era of elderlings, yet there the river is same height and boathouse is near shore... Did the elderlings build it far up from the shore, or did that single exit mysteriously not sink like the rest of the city?

Hm, I'm not sure, but I thought the boat house is a bit deeper and some boats are destroyed but in the end Malta and maybe the other girl (forgot her name) carry the boat up to the "island" they are standing on...